This study investigated students’ perceptions of their behavioural and emotional self-regulation after a six-to-eight week implementation of classroom physical activity breaks (CPAB). It also explored students’ perceptions of their affective states before and after CPAB, as well as their interest and engagement during CPAB. Eighty-two elementary students aged from 6 to 10 years filled in booklets each week during the study. Among them, 14 students with behavioural difficulties as experimental group and 14 students as control group completed the Self-Regulation Questionnaire at the beginning and the end of the experimental design. Repeated measure ANOVA revealed an interaction effect (condition X group) on emotional self-regulation among students with behavioural difficulties compared to their peers after CPAB. A descriptive analysis of the booklets revealed the positive reactions of students to CPAB, especially those with behavioural difficulties. These findings thus support the value of CPAB for students with behavioural difficulties, and open new perspectives of research.